package MyHelper;

public class Test {

	/**
	 * @param args
	 */
	public static void main(String[] args) {
		String hostname="genome-mysql.cse.ucsc.edu";
		String db="hg19";
		
		/*Doan code sau la xu ly cho cac glicolytic gene*/
		
		//GeneInformation myGene = new GeneInformation();
		//step1 convert input gene list to list of full info genes
		//myGene.geneListToGeneInFile("data/glycolytic/orgList/glycolytic_genes.txt","data/glycolytic/refGeneInfo/Glycolytic_genes_full.txt","refGene");
		
		//step2 chuyen tu gene list sang cac files moi file chua neighbors cua 1 gene
		//myGene.getNeighborsOfList("data/glycolytic/refGeneInfo/Glycolytic_genes_full.txt","refGene", "data/glycolytic/refGeneNeighbours");
		
		//step 3 chuyen tu gene sang gene co kem proteinID (refGene -> knownGen)
		//myGene.geneDirToProteinDir("data/glycolytic/refGeneNeighbours", "data/glycolytic/knownGeneInfo");
		
		//step4 chich nguyen proteinID va genepos
		//myGene.hg19KnownGene2ProtetinID_D2D("data/glycolytic/knownGeneInfo","data/glycolytic/protDir");
		
		//myGene.refGeneToName2("data/glycolytic/refGeneInfo/Glycolytic_genes_full.txt", "data/glycolytic/refGeneInfo/Glycolytic_genes_name2.txt");
		
		/*Doan code sau la de xu ly 2 file tu ChEMBL*/
		//Step1 get the protID
		//ChEMBLHelper.ChEmbl2ProteinIDinFile("data/transporter/ChEMBL_org/amino_acid_transporters_human.fa", "data/transporter/ChEMBL_ProtID/amino_acid_transporters_human.txt");
		//ChEMBLHelper.ChEmbl2ProteinIDinFile("data/transporter/ChEMBL_org/sugar_transporters_human.fa", "data/transporter/ChEMBL_ProtID/sugar_transporters_human.txt");
		
		//Step2 get info from protID
		//ChEMBLHelper.protIDList2GeneList("data/transporter/ChEMBL_ProtID/amino_acid_transporters_human.txt", "data/transporter/ChEMBL_ProtID2KnownGene/amino_acid_transporters_human.txt");
		//ChEMBLHelper.protIDList2GeneList("data/transporter/ChEMBL_ProtID/sugar_transporters_human.txt", "data/transporter/ChEMBL_ProtID2KnownGene/sugar_transporters_human.txt");
		
		//Step3 get info of gene from refGene Table
		//ChEMBLHelper.known2ref("data/transporter/ChEMBL_ProtID2KnownGene/amino_acid_transporters_human.txt", "data/transporter/ChEMBL_KnownGene2RefGene/amino_acid_transporters_human.txt");
		//ChEMBLHelper.known2ref("data/transporter/ChEMBL_ProtID2KnownGene/sugar_transporters_human.txt", "data/transporter/ChEMBL_KnownGene2RefGene/sugar_transporters_human.txt");
		
		//step 4 get neighbours of genes
		GeneInformation myGene = new GeneInformation();
		myGene.getNeighborsOfList("data/transporter/ChEMBL_KnownGene2RefGene/amino_acid_transporters_human.txt","refGene", "data/transporter/ChEMBL_RefGeneNeighbors");
		myGene.getNeighborsOfList("data/transporter/ChEMBL_KnownGene2RefGene/sugar_transporters_human.txt","refGene", "data/transporter/ChEMBL_RefGeneNeighbors");
		
		//step 5 from genes get the proteins (also th position of the gene)
		//this now only for human
		//GeneInformation tp_genes = new GeneInformation();
		//tp_genes.geneDirToProteinDir("data/transporter/ChEMBL_RefGeneNeighbors", "data/transporter/ChEMBL_RefGenNeighbors2KnowGene");
		
		//step6 chi lay lai proteinID tu cac file kq cua step 5
		//GeneInformation tp_genes_pID = new GeneInformation();
		//tp_genes_pID.hg19KnownGene2ProtetinID_D2D("data/transporter/ChEMBL_RefGenNeighbors2KnowGene", "data/transporter/ChEMBL_Neighboring_ProtID");
	}

}
